The inception of the now completed Human Genome Project has spurred an explosion in genomic research. DNA expression arrays, and other genomic tools were created to take advantage of the wealth of information promised, and currently provided by a completely sequenced human genome. As a result, genomics has come to dominate the biological landscape. Genomics, however, has its limits. Now more than ever, it is becoming clear that gene sequence alone cannot predict the fate or behavior of protein products. Though high throughput transcriptional profiling on DNA chips or microarrays can be used to determine when, where, and how much RNA is transcribed, there is rarely a relationship between RNA transcription and protein expression.1,2,3 Post transcriptional modifications such as phosphorylation, and mRNA and peptide degradation can alter the function and concentration of a protein and are invisible to transcriptional profiling.
This gap between genomics and cellular behavior impedes elucidation of protein function as well as the identification of novel drug targets. Research in the post genomic era, then, will require a bridge between genomics and cellular behavior. Proteomics, which goal is to study the protein products of the genome, promises to be this bridge. By taking advantage of newly developed analytical tools, proteomics strives to study the dynamic, protein equivalent of the genome, the proteome. In so doing, proteomics would provide fundamental information on the molecular workings of the cell, as well the ability to observe the effect that specific diseases or drug treatments have on protein cascades.4 Indeed, the potential ability of proteomics to provide information about proteins on a global scale is tremendous for pharmaceutical research, as over 75% of the predicted proteins in multicellular organisms have no known cellular function5 and as many as 4,000 protein drug targets are predicted.6 
Fundamental to proteomics are the abilities to both separate and identify proteins. Currently separation is achieved via several methods, the most popular being two dimensional gel electrophoresis (2-DE).7 Separation by 2-DE is on the basis of charge (isoelectric focusing) and size (PAGE). Gels are stained by a variety of methods, including Coomassie blue stain, silver stain, fluorescent dyes, and radio labels. Once the gel is stained, proteins are easily located and excised from the gel. Currently, the most effective method for protein identification is by mass spectrometry (MS). The sensitivity of mass spectrometry, coupled with recently developed ionization methods, allows for accurate protein characterization and identification. Indeed, advancements in mass spectrometry are responsible for the growth of proteomics as a field.
The now inseparable relationship between mass spectrometry and proteomics can be traced to two technological breakthroughs in the late 1980's: electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI).8,9,10 In contrast to previous ionization methods, both ESI and MALDI are “soft” ionization methods, capable of generating ions from proteins and peptides without significant fragmentation. So soft are ESI and MALDI as ionization methods, that under certain conditions even non-covalent interactions are undisturbed, allowing for the analysis of large multi-protein complexes.11 ESI is easily coupled to liquid phase chromatographic and electrophoric techniques, a quality for which the method quickly gained popularity. Due to this, and the method's tendency to produce multiple charged ions allowing detection outside the nominal m/z range of simple instruments, ESI soon became the method of choice for analysis of proteins in the liquid phase.12,13 
Ions produced via MALDI are, in contrast, largely singly charged, providing mass spectra that are easily interpreted. Furthermore, the time-of flight (TOF) mass analyzer to which MALDI is most often coupled is robust, simple, sensitive, and capable of detecting proteins as large as 100,000 mass units (amu).14,15 Both methods are now established as state of the art analytical tools in proteomics, finding applications in protein identification by mass mapping, and single peptide fragmentation, as well as the identification and characterization of post-translation modifications such as protein phosphorylation.13 Perhaps the most popular of these applications is protein identification by mass mapping, in which proteins, once separated by 2-DE or HPLC, are digested by a sequence-specific proteolytic enzyme such as trypsin. Upon digestion by such an enzyme, a specific protein will produce a unique set of polypeptide sequences, which upon detection and analysis by MS, yields a polypeptide mass-map. This mass-map, which is unique, can be used to identify the protein. Peptide mass-mapping has been used in the proteomic analysis of Haemophilus influenzae as well as several strains of yeast used in the brewing industry.16 Mass spectrometry is also used for protein sequencing, replacing Edman sequencing. Mass spectrometry allows for the analysis of subfemtomole quantities and is not restricted by N-terminal modifications, both problems associated with the Edman-based method.17 
Neither ESI nor MALDI, however, are without limitations. Due to the attomolar sensitivity of both ESI and MALDI, and the small volume of MS samples, cleanliness of biological samples is perhaps the greatest limitation for proteomic MS.18,19 This limitation is particularly noticeable in proteomics as protein samples obtained from 2-DE gel digestion contain salts, ionic detergents and involatile solvents that can greatly reduce signal intensity and resolving power.20 The importance of sample cleaning and preparation is in fact so great that the literature abounds with novel sample prep protocols, particularly for the more popular MALDI method.21,22,23 
Furthermore, the emergence of products specifically targeted at sample preparation for proteomic MS highlights the significance of this step. Millipore (Bedford, Mass.) has introduced the ZipTiP™, a 10 μl pipette tip packed with a polymer stabilized expanded bed (PSEB) of C18 reverse phase chromatographic media. When a protein or peptide sample is introduced into the pipette, peptides are captured by the C18 media via hydrohobic interactions. The sample can then be washed of impurities and subsequently eluted.19 Sample cleaning with ZipTiP™ technology has been shown to significantly improve the signal-to noise ratio of peptide mass maps obtained from MALDI-TOF.22 
Sample cleaning has also been achieved by assembling reverse-phase media directly onto the MALDI probe. A stainless steel MALDI probe is coated with gold, and then self-assembled monolayers (SAMs) are created by taking advantage of gold-thiol chemistry. At present, both C18 and ionic reverse phase media have been created.23,24 Although both of these methods achieve sample cleaning and improve spectrum quality, they nonetheless fail to do so in high throughput fashion. Proteomics is a high throughput field and the need to individually purify and analyze samples with MS is severely limiting.7 With this in mind, Bruker (Bremen, Germany) has designed the Anchor Chip, a MALDI target with 384 individual hydrophilic anchors. The Anchor Chip is stainless steel with a hydrohobic coating that allows for protein and peptide capture. Samples are spotted with a water insoluble matrix such as α-cyano 4-hydroxycinnamic acid (HCCA), and then washed. Samples are then re-dissolved and allowed to crystallize, whereupon they shrink to the hydrophilic anchor.25 Despite allowing for high throughput in sample preparation and MS analysis, the anchor chip is cost prohibitive, and requires stringent washing prior to re-use. Furthermore, the presence of 384 liquid targets on a flat surface increases the possibility of cross-contamination.
In order to eliminate the bottle-neck of proteomic sample preparation, a high throughput tool is required. Ideally, this tool should be both inexpensive and disposable. Most importantly, the tool should reduce sample cross-contamination. The present invention overcomes problems in the art by providing such a tool.